Claude skill · cast freeform-summary-to-galaxy-data-flow
Translate a free-form source summary into a Galaxy data-flow design brief.
← All cast skills · Source mold →
Install
/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry
Then invoke as:
/foundry-skills:freeform-summary-to-galaxy-data-flow
Skill Bundle
/ packaged cast
- attached files
- 6
- upfront
- 1
- on demand
- 5
- cast rev
- n/a
- validated
- 0
Produces: 1 artifact.
Consumes: 2 artifacts.
Artifact Contract
/ skill handoff Produces
freeform-galaxy-data-flow
Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions.
markdownfreeform-galaxy-data-flow.md
Raw artifact contract
{
"id": "freeform-galaxy-data-flow",
"kind": "markdown",
"default_filename": "freeform-galaxy-data-flow.md",
"description": "Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions."
}
Consumes
freeform-summary
Free-form source summary emitted by [[summarize-paper]] or [[interview-to-freeform-summary]]; consumed alongside the Galaxy interface brief.
Raw artifact contract
{
"id": "freeform-summary",
"description": "Free-form source summary emitted by [[summarize-paper]] or [[interview-to-freeform-summary]]; consumed alongside the Galaxy interface brief.",
"producers": [
"interview-to-freeform-summary",
"summarize-paper"
]
}
freeform-galaxy-interface
Preceding Galaxy interface brief from [[freeform-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.
Raw artifact contract
{
"id": "freeform-galaxy-interface",
"description": "Preceding Galaxy interface brief from [[freeform-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.",
"producers": [
"freeform-summary-to-galaxy-interface"
]
}
Attached Files
/ runtime references Load upfront
Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.
upfront runtime verbatim hypothesis deterministic 6.5 KB
- bundle
references/notes/galaxy-data-flow-draft-contract.md- source
content/research/galaxy-data-flow-draft-contract.md
Preview md
---
type: research
subtype: design-spec
title: "Galaxy data-flow draft contract"
tags:
- research/design-spec
- target/galaxy
status: draft
created: 2026-05-02
revised: 2026-05-03
revision: 2
ai_generated: true
related_notes:
- "[[nextflow-to-galaxy-channel-shape-mapping]]"
- "[[nextflow-operators-to-galaxy-collection-recipes]]"
- "[[galaxy-workflow-draft]]"
related_molds:
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[cwl-summary-to-galaxy-data-flow]]"
- "[[freeform-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
- "[[cwl-summary-to-galaxy-template]]"
- "[[freeform-summary-to-galaxy-template]]"
- "[[compare-against-iwc-exemplar]]"
- "[[advance-galaxy-draft-step]]"
sources:
- "https://github.com/galaxyproject/foundry/issues/54"
summary: "Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation."
---
# Galaxy Data-Flow Draft Contract
This is an architectural contract, not a schema. Evidence is strongest for Mold and Pipeline boundaries. Proposed fields are speculative until exercised by two or three worked translations.
## Boundary
The data-flow draft owns a target-shaped abstract DAG for Galaxy. It should not be valid `gxformat2` and should not resolve exact Tool Shed tools.
Data-flow draft owns:
- Galaxy-facing workflow inputs and outputs.
- Abstract nodes, edges, branches, collection mapping, collection reduction, and placeholder transformations.
- Input/output shape decisions such as `File`, `list`, `paired`, `list:paired`, or `list:list`.
- Conceptual Galaxy idioms: map-over, reduction, Apply Rules, collection cleanup, identifier synchronization, tabular bridge.
- Abstract unresolved tool needs with input and output shapes.
- Confidence and rat
...
Load on demand
Ground collection-shape choices in curated, corpus-observed operation and recipe patterns.
Trigger: When selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.
on-demand runtime verbatim corpus-observed deterministic 4.6 KB
- bundle
references/patterns/galaxy-collection-patterns.md- source
content/patterns/galaxy-collection-patterns.md
Preview md
---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: collection patterns"
aliases:
- "Galaxy collection pattern MOC"
- "collection transformation patterns"
- "IWC collection pattern map"
tags:
- pattern
- target/galaxy
- topic/galaxy-transform
- topic/collection-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
ai_generated: true
summary: "Use this MOC to choose corpus-grounded Galaxy collection transformation patterns."
related_notes:
- "[[iwc-transformations-survey]]"
- "[[iwc-conditionals-survey]]"
related_patterns:
- "[[manifest-to-mapped-collection-lifecycle]]"
- "[[cleanup-sync-and-publish-nonempty-results]]"
- "[[reshape-relabel-remap-by-collection-axis]]"
- "[[fan-in-bundle-consume-and-flatten]]"
- "[[collection-cleanup-after-mapover-failure]]"
- "[[sync-collections-by-identifier]]"
- "[[harmonize-by-sortlist-from-identifiers]]"
- "[[regex-relabel-via-tabular]]"
- "[[relabel-via-rules-and-find-replace]]"
- "[[collection-swap-nesting-with-apply-rules]]"
- "[[collection-split-identifier-via-rules]]"
- "[[collection-build-list-paired-with-apply-rules]]"
- "[[tabular-to-collection-by-row]]"
- "[[tabular-concatenate-collection-to-table]]"
- "[[tabular-pivot-collection-to-wide]]"
related_molds:
- "[[implement-galaxy-tool-step]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[cwl-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
- "[[cwl-summary-to-galaxy-template]]"
- "[[freeform-summary-to-galaxy-template]]"
- "[[compare-against-iwc-exemplar]]"
---
# Galaxy: collection patterns
This is the runtime-facing map for Galaxy collection transformation choices. Use it before loading raw survey notes. The survey remains evidence backin
...
Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns.
Trigger: When data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.
on-demand runtime verbatim corpus-observed deterministic 2.6 KB
- bundle
references/patterns/galaxy-conditionals-patterns.md- source
content/patterns/galaxy-conditionals-patterns.md
Preview md
---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: conditionals patterns"
aliases:
- "Galaxy conditional pattern MOC"
- "Galaxy when patterns"
- "conditional workflow patterns"
tags:
- pattern
- target/galaxy
- topic/galaxy-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
ai_generated: true
summary: "Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns."
related_notes:
- "[[iwc-conditionals-survey]]"
related_patterns:
- "[[conditional-run-optional-step]]"
- "[[conditional-route-between-alternative-outputs]]"
- "[[conditional-gate-on-nonempty-result]]"
- "[[conditional-transform-or-pass-through]]"
- "[[collection-cleanup-after-mapover-failure]]"
related_molds:
- "[[implement-galaxy-tool-step]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[cwl-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
- "[[cwl-summary-to-galaxy-template]]"
- "[[freeform-summary-to-galaxy-template]]"
- "[[compare-against-iwc-exemplar]]"
---
# Galaxy: conditionals patterns
This is the runtime-facing map for Galaxy conditional workflow choices. Use it before loading raw survey notes. The survey remains evidence backing; the operation and recipe pages are the actionable references.
## Direct Gates
- [[conditional-run-optional-step]] — expose or derive a boolean, connect it as `inputs.when`, and use `when: $(inputs.when)` to skip optional steps.
- [[conditional-gate-on-nonempty-result]] — compute a boolean from empty/non-empty dataset or collection state before gating downstream reporting/export. The MGnify recipe is corpus-backed but clunky pending verified-pattern workflow work.
## Routes and Fallbacks
- [[conditional-route-between-alternati
...
Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes.
Trigger: When the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.
on-demand runtime verbatim corpus-observed deterministic 5.3 KB
- bundle
references/patterns/galaxy-interval-patterns.md- source
content/patterns/galaxy-interval-patterns.md
Preview md
---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: genomic interval patterns"
aliases:
- "Galaxy interval pattern MOC"
- "genomic interval transformation patterns"
- "IWC interval pattern map"
tags:
- pattern
- target/galaxy
- topic/galaxy-transform
- topic/interval-transform
status: draft
created: 2026-06-10
revised: 2026-06-10
revision: 1
ai_generated: true
summary: "Use this MOC to choose corpus-grounded Galaxy genomic interval operations and recipes on coordinate features."
related_notes:
- "[[iwc-interval-operations-survey]]"
related_patterns:
- "[[interval-overlap-filter]]"
- "[[interval-coverage]]"
- "[[interval-merge-overlapping]]"
- "[[interval-window-flank]]"
- "[[interval-consensus-by-multi-intersect]]"
- "[[interval-mask-by-set-algebra]]"
- "[[interval-windowed-coverage]]"
- "[[tabular-synthesize-bed-from-3col]]"
related_molds:
- "[[implement-galaxy-tool-step]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[cwl-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
- "[[cwl-summary-to-galaxy-template]]"
- "[[paper-summary-to-galaxy-template]]"
- "[[compare-against-iwc-exemplar]]"
---
# Galaxy: genomic interval patterns
The runtime-facing map for Galaxy **coordinate-feature** choices — operations that understand `chrom/start/end/strand`, as opposed to opaque-column [[galaxy-tabular-patterns]] or container-shaped [[galaxy-collection-patterns]]. Use it before loading raw survey notes; [[iwc-interval-operations-survey]] is the evidence backing, these pages are the actionable references.
This is the smallest of the three data-shape MOCs by design. Interval algebra is a real but moderate cluster in IWC — concentrated in epigenetics peak-consensus and SARS-CoV-2 mask
...
Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns.
Trigger: When data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.
on-demand runtime verbatim corpus-observed deterministic 3.3 KB
- bundle
references/patterns/galaxy-tabular-patterns.md- source
content/patterns/galaxy-tabular-patterns.md
Preview md
---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: tabular patterns"
aliases:
- "Galaxy tabular pattern MOC"
- "tabular transformation patterns"
- "IWC tabular pattern map"
tags:
- pattern
- target/galaxy
- topic/galaxy-transform
- topic/tabular-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
ai_generated: true
summary: "Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns."
related_notes:
- "[[iwc-tabular-operations-survey]]"
related_patterns:
- "[[tabular-filter-by-column-value]]"
- "[[tabular-filter-by-regex]]"
- "[[tabular-cut-and-reorder-columns]]"
- "[[tabular-compute-new-column]]"
- "[[tabular-join-on-key]]"
- "[[tabular-group-and-aggregate-with-datamash]]"
- "[[tabular-sql-query]]"
- "[[tabular-prepend-header]]"
- "[[tabular-synthesize-bed-from-3col]]"
- "[[tabular-split-taxonomy-string]]"
- "[[tabular-relabel-by-row-counter]]"
- "[[tabular-to-collection-by-row]]"
- "[[tabular-concatenate-collection-to-table]]"
- "[[tabular-pivot-collection-to-wide]]"
related_molds:
- "[[implement-galaxy-tool-step]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[cwl-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
- "[[cwl-summary-to-galaxy-template]]"
- "[[freeform-summary-to-galaxy-template]]"
- "[[compare-against-iwc-exemplar]]"
---
# Galaxy: tabular patterns
This is the runtime-facing map for Galaxy tabular transformation choices. Use it before loading raw survey notes. The survey remains evidence backing; the operation pages are the actionable references.
## Row And Column Operations
- [[tabular-filter-by-column-value]] — keep/drop rows by string column value with `Filter1`.
- [[tabular-filter-by-regex]]
...
Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it.
Trigger: When the interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or the free-form summary describes per-sample/per-record metadata that must survive map-over steps.
on-demand runtime verbatim corpus-observed deterministic 8.4 KB
- bundle
references/notes/galaxy-sample-sheet-collections.md- source
content/research/galaxy-sample-sheet-collections.md
Preview md
---
type: research
subtype: component
title: "Galaxy sample_sheet collection types"
tags:
- research/component
- target/galaxy
status: draft
created: 2026-05-05
revised: 2026-05-06
revision: 2
ai_generated: true
related_notes:
- "[[galaxy-collection-semantics]]"
- "[[galaxy-collection-tools]]"
- "[[nextflow-workflow-io-semantics]]"
- "[[nextflow-params-to-galaxy-inputs]]"
- "[[nextflow-path-glob-to-galaxy-datatype]]"
- "[[nextflow-to-galaxy-channel-shape-mapping]]"
- "[[nextflow-to-galaxy-reference-data-mapping]]"
related_molds:
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
sources:
- "Galaxy PR #19305 (Implement Sample Sheets), merged 2025-07-30"
- "lib/galaxy/model/dataset_collections/types/sample_sheet.py"
- "lib/galaxy/model/dataset_collections/types/sample_sheet_util.py"
- "lib/galaxy/model/dataset_collections/type_description.py"
- "lib/galaxy/schema/schema.py (SampleSheetColumnDefinition, SampleSheetRow)"
- "lib/galaxy/tools/wrappers.py (DatasetCollectionWrapper.sample_sheet_row)"
- "lib/galaxy/tools/sample_sheet_to_tabular.xml"
- "lib/galaxy/webapps/galaxy/api/dataset_collections.py (sample_sheet_workbook endpoints)"
- "lib/galaxy/model/migrations/alembic/versions_gxy/3af58c192752_implement_sample_sheets.py"
summary: "Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist."
---
# Galaxy sample_sheet collection types
Reference for the Galaxy backend shape that targets structured per-row metadata — the natural landing zone for Nextflow `samplesheetToList` parameters and for any source-side idiom that pairs typed metadata columns with dataset references.
## Shape
A `sample_sheet` is a list-shaped collection where each el
...
SKILL.md
# freeform-summary-to-galaxy-data-flow
Follow the procedure below and use the artifact/reference sections as the runtime contract.
## When To Use
- Translate a free-form source summary into a Galaxy data-flow design brief.
## Inputs
- Read artifact `freeform-summary`. Produced by `interview-to-freeform-summary`, `summarize-paper`. Free-form source summary emitted by summarize-paper or interview-to-freeform-summary; consumed alongside the Galaxy interface brief.
- Read artifact `freeform-galaxy-interface`. Produced by `freeform-summary-to-galaxy-interface`. Preceding Galaxy interface brief from freeform-summary-to-galaxy-interface that pins inputs, outputs, and labels.
## Outputs
- Write artifact `freeform-galaxy-data-flow` as `freeform-galaxy-data-flow.md`. Format: `markdown`. Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions.
## Required Tools
- None declared. Procedure should not assume external CLIs are present.
## Load Upfront
- `references/notes/galaxy-data-flow-draft-contract.md`: Research note copied verbatim into the bundle. Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.
## Load On Demand
- `references/patterns/galaxy-collection-patterns.md`: Pattern note copied verbatim into the bundle. Ground collection-shape choices in curated, corpus-observed operation and recipe patterns. Use when: selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.
- `references/patterns/galaxy-conditionals-patterns.md`: Pattern note copied verbatim into the bundle. Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns. Use when: data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.
- `references/patterns/galaxy-interval-patterns.md`: Pattern note copied verbatim into the bundle. Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes. Use when: the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.
- `references/patterns/galaxy-tabular-patterns.md`: Pattern note copied verbatim into the bundle. Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns. Use when: data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.
- `references/notes/galaxy-sample-sheet-collections.md`: Research note copied verbatim into the bundle. Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it. Use when: the interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or the free-form summary describes per-sample/per-record metadata that must survive map-over steps.
## Validation
- None declared.
## Procedure
Read a free-form source summary plus the preceding Galaxy interface brief and emit a reviewable Markdown data-flow brief. Capture abstract operations, collection map/reduce choices, shape-changing placeholder transformations, unresolved Galaxy tool needs, confidence, and open questions.
Free-form sources rarely give enough to fix exact operations. Translate what the summary and interface brief support, classify the rest as unresolved tool needs or open questions, and do not present narrative intent as already-decided Galaxy wiring.
The output is not gxformat2 and should not resolve exact Tool Shed tools. freeform-summary-to-galaxy-template turns this handoff and the interface brief into a skeleton.
## Runtime Notes
- Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
- Preserve declared artifact filenames unless the user or harness supplies explicit paths.
- Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.